It is not explicitly stated how these designations were assigned, though it is generally assumed that they were simply incremental, each newly encountered species getting a number one higher than the previous. This mostly holds up when comparing numbers to probable first contact dates or vicinity to Borg space, though some anomalies exist, most notably the Alpha Quadrant species Ferengi having an unusually low number of 180 (which may suggest that at least one Ferengi ship had visited the Delta Quadrant and encountered the Borg early on in the Borg's expansion). Numbers appear to have been assigned at first contact, and don't seem to have been reused even after the whole species was assimilated.

In Star Trek: Voyager - Elite Force, Seven of Nine mentions Species 1567, which was engaged in a long range war. They used automated gunships called dreadnoughts in order to defeat their enemy. One of them was transported to the "Forge" where a mission took place in the game.